Phenotype and GWAS Information:

Agronomic Traits

Note: All the agronomic trait is from the article Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.

Metabolic Traits

Note: All the metabolic trait is from the article Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Some metabolics have two replications, the second replication is end with '_2', like 'mr1002_2'.

Search Results:

The detailed information about mr1917 can be find at here.

GWAS Results:

Note: If the P-value of Linear Regression (LR) or Linear Mixed Model (LMM) ≤ 1e-5 or the rank ≤ 20000, the results are saved. Only the LMM results are plotted below.

Significant Candidate Loci (Lead SNP):

Variation IDVariation ID V6ChromosomePositionLR P-value LMM P-value
vg1008474924 sf1008403786 10 8474924 3.88E-10 3.75E-08
vg1009371286 sf1009300107 10 9371286 4.62E-10 2.20E-08
vg0407825687 sf0407820955 4 7825687 8.32E-10 8.86E-08
vg1006519679 sf1006535302 10 6519679 3.22E-09 5.80E-08
vg0407830709 sf0407825977 4 7830709 4.17E-09 1.57E-07
vg1005658705 sf1005675243 10 5658705 6.28E-09 4.05E-06
vg1210581967 sf1210579380 12 10581967 9.45E-09 4.19E-06
vg0807119511 sf0807118516 8 7119511 1.05E-08 6.90E-07
vg0220854116 sf0220848248 2 20854116 6.90E-08 5.46E-07
vg1216843502 sf1216837456 12 16843502 1.14E-07 1.19E-06
vg0316618971 sf0316617616 3 16618971 2.04E-07 6.38E-07
vg0414193101 sf0414183817 4 14193101 2.28E-07 2.34E-07
vg1007118237 sf1007133860 10 7118237 2.75E-07 4.12E-07
vg0220823492 sf0220817624 2 20823492 3.55E-07 2.80E-06
vg0216564726 sf0216558856 2 16564726 8.51E-06 4.70E-06
vg0222734635 sf0222728766 2 22734635 NA 3.34E-08
vg0222719727 sf0222713858 2 22719727 NA 4.39E-07
vg0222911545 sf0222905676 2 22911545 NA 2.74E-06